Phenotype management: a new approach to habitat restoration

Conservation and the genetics of populations

Phenotypic diversity is considered beneficial to the evolution of contingent cooperation, in which cooperators channel their help preferentially towards others of similar phenotypes. However, it remains largely unclear how phenotypic variation arises in the first place and thus leads to the construction of phenotypic complexity. Here we propose a mathematical model to study the coevolutionary dynamics of phenotypic diversity and contingent cooperation. Unlike previous models, our model does not assume any prescribed level of phenotypic diversity, but rather lets it be an evolvable trait. Each individual expresses one phenotype at a time and only the phenotypes expressed are visible to others. Moreover, individuals can differ in their potential of phenotypic variation, which is characterized by the number of distinct phenotypes they can randomly switch to. Each individual incurs a cost proportional to the number of potentially expressible phenotypes so as to retain phenotypic variation and expression. Our results show that phenotypic diversity coevolves with contingent cooperation under a wide range of conditions and that there exists an optimal level of phenotypic diversity best promoting contingent cooperation. It pays for contingent cooperators to elevate their potential of phenotypic variation, thereby increasing their opportunities of establishing cooperation via novel phenotypes, as these new phenotypes serve as secret tags that are difficult for defector to discover and chase after. We also find that evolved high levels of phenotypic diversity can occasionally collapse due to the invasion of defector mutants, suggesting that cooperation and phenotypic diversity can mutually reinforce each other. Thus, our results provide new insights into better understanding the coevolution of cooperation and phenotypic diversity.

The United Nations General Assembly declared 2021–2030 as the “Decade of Ecosystem Restoration”, which positions “the restoration of ecosystems as a major nature-based solution towards meeting a wide range of global development goals and national priorities”. Ecological restoration, when it was implemented effectively, contributes to improving food and water security, mitigating climate change, protecting biodiversity, boosting economic prosperity and benefiting human health and well-being. Thus, ecological restoration is fundamental for the success of ecological civilization and sustainable development. Ecological restoration theories in developed countries usually require restoring the ecosystem to the status prior to degradation, and this requirement is difficult to achieve in regions with serious degradation, especially in developing countries. We developed a new theory of ecological restoration, or stepwise ecological restoration (STERE), which comprises three modes in different restoration stages: Environmental remediation in the initial stage with serious degradation, ecological rehabilitation for moderately degraded ecosystems, and natural restoration for slightly degraded ecosystems. Environmental remediation aims to reduce environmental pollution through the removal or detoxification of pollutants or excess nutrients from soil and water. Ecological rehabilitation is the process of assisting the recovery of an ecosystem that has been degraded, damaged, or destroyed through various physical, chemical and biological restoration strategies. Natural restoration aims to restore ecosystem functions and services and improve ecosystem resilience without much human assistance. Environmental remediation is fundamental and needs to be implemented prior to ecological rehabilitation and natural restoration in places where pollution is severe. Only the former is successfully carried out; however, when the ecosystem is moderately degraded, ecological rehabilitation can be effectively implemented. In places where the ecosystem is slightly degraded, natural restoration is recommended. The processes of ecological rehabilitation and natural restoration will result in ecological functions that are more complete, an increase in biodiversity, and improved ecosystem resilience. For STERE, appropriate restoration goals should be formulated based on the degree of degradation, local funding support, and technological development. The new theory proposed in this study emphasizes the application of reference ecosystems in restoration projects and the importance of ecological monitoring. It also requires an adaptive restoration management framework that considers the influence of global climate change. STERE should be implemented for future ecosystems rather than only for restoring an ecosystem to a status similar to the condition prior to degradation. Moreover, STERE promotes systematic large-scale landscape restoration by considering the interactions between individual small scales (e.g., field scale) and large scales (e.g., catchment scale). In addition, technologies such as unmanned aerial vehicles and remote sensing should be more widely used in future STERE projects. Ecological restoration databases should be established for restorative activities in mountains, waters, forests, farms, lakes and other ecosystems. The newly proposed STERE theory would play an important role in developing restoration projects worldwide, especially in developing countries.

Effects of forest fragmentation on the effective and realized gene flow of Neotropical tree species: implications for genetic conservation

基于恢复生态学的泰山地区“山水林田湖草”生态修复研究

In Atlantic salmon, as in most salmonids, males can mature early in the life cycle, as small freshwater fish, termed parr, and/or undergo a sea migration before maturing as full-size adults. The alternative life histories are contingent on environmental and social circumstances, such as growth rate, territory quality or any other factor that affects the individual's state. In order to model the choice of life history in this group of commercially valuable species, it is necessary to understand not only the relative contribution of the different male types to subsequent generations, but also to know the factors that affect reproductive success in each type. In this paper we present the results of a study designed to investigate the factors that affect the reproductive success of mature parr. We used highly polymorphic minisatellite DNA markers to analyse paternity in a series of mating experiments where the number and body size of parr were manipulated. The fraction of eggs fertilized by mature parr ranged from 26 to 40 per cent, with individual parr fertilizing up to 26 per cent of the eggs. A strong positive correlation was found between parr size and reproductive success. The relative success of parr decreased with increasing parr number. Data from this and other studies on variation in the timing and degree of parr reproductive success are discussed in relation to the evolution of male mating strategies and life history in salmonids.

Ecological restoration is alive and well in New Zealand. Selecting for web pages from New Zealand, Google yields 33 600 results using the words ‘ecological restoration’, whereas Google Scholar yields 22 100 results. The New Zealand Ecological Restoration Network (http://www.nzern.org.nz) comprises 240 conservation groups with 450 community led conservation projects, whereas the Department of Conservation (http://www.doc.govt.nz) manages a diversity of restoration projects covering tens of thousands of hectares, both on offshore islands and on the mainland. In addition, a wide range of other government and non-government organizations, including an increasing number of businesses, are involved in restoration projects on both private and public land, including some of the largest restoration projects in New Zealand such as the 3400 ha Maungatautari Ecological Island project (http://www.maungatrust.org). Eight New Zealand restoration projects were recently included in the Global Restoration Networks listing of the 25 top restoration projects in Australasia (http://www.globalrestorationnetwork.org/countries/australianew-zealand/). So what does ecological restoration involve in New Zealand? Perhaps, the best way to address this is to consider what the key threats are to indigenous biodiversity. Without a doubt, the most significant current threat is from invasive species that are now naturalized in New Zealand (Allen & Lee 2006). The introduced animals of greatest threat to indigenous biodiversity are mammalian herbivores (ungulates, lagomorphs, brushtail possums, wallabies) and carnivores (rodents, mustelids, cats, hedgehogs). While habitat loss has been a major issue historically, it is much less of a threat today, although the legacies of historical clearing still persist, especially in the small, isolated and often degraded remnants that occur in the most developed parts of New Zealand. As is the case worldwide, approaches to ecological restoration are many and varied. In New Zealand, these can be broadly grouped into three categories, although it would be fair to say that many restoration projects include elements of all three: Intensive management of highly degraded sites through the deliberate introduction and establishment of new individuals of indigenous plant and animal species. This approach is especially important at sites degraded by activities such as farming or mining and usually involves planting and/or direct-seeding. Control of domestic and invasive herbivores is usually essential to ensure that plantings and seedings are successful. The restoration of the 220 ha Tiritiri Matangi Island near Auckland is a good example of this approach (http://www.tiritirimatangi.org.nz). Minimum interference management. This is most commonly applied to formerly farmed land from which domestic livestock (primarily cattle and sheep) have been excluded and regeneration to indigenous forest occurs without direct planting or seeding, although control of mammalian pests is often required to promote regeneration. Hinewai Reserve covering more than 1000 ha on Banks Peninsula east of Christchurch is one of the best-known examples of this approach (Wilson 2004). Intensive management of relatively natural sites that have been, or are being, degraded by introduced species, particularly introduced mammals. Many of these sites are relatively natural in that they are still dominated by indigenous vegetation (e.g. forest), but many of their constituent species, both plant and animal, have been lost or severely reduced in abundance due to predation. These projects are often referred to as mainland islands (Saunders & Norton 2001), although a wide range of projects are subject to intensive predator management. The first two approaches focus primarily on redressing historical habitat loss through improving connectivity between remnants, enhancing buffers around remnants, and creating additional habitat. The third category specifically addresses the impacts of invasive animal species. Notwithstanding this distinction, what is common to all three approaches is a strong focus on predator management. The pervasive impact of predators is such that without appropriate management, it is not possible to enhance indigenous biodiversity values in either degraded or predominantly natural sites. There is also an increasing focus on the management of invasive plants, especially in more degraded sites, as these species can alter successional trajectories or result in restoration failure through direct competition with planted species. What distinguishes ecological restoration in New Zealand from many other parts of the world is the strong focus on the management of invasive species in order to provide habitat for a flora and especially fauna that has been undergoing rapid decline since settlement by Polynesians (some 750 years ago) and later, Europeans. Factors such as an absence of mammalian predators and extended faunal life histories with low reproductive rates have made the fauna in particular very vulnerable to invasive mammals. Early efforts to restore biodiversity threatened by invasive species focused on islands where predator control is potentially achievable without fencing, but more recently the emphasis has shifted to the mainland where efforts have gone into creating mainland areas that are kept free of predators (mainland islands). Mainland islands involve either intensive predator control or increasingly, the use of predator-proof fences. The longest predator proof fence to date (47 km) surrounds the 3500 ha Maungatautari mainland island. This emphasis on predator management should not, however, be seen as the only component of ecological restoration in New Zealand. Numerous projects throughout the country focus on restoring degraded sites, especially previously farmed sites, with the objective of reestablishing indigenous plant and animal communities. Some of these projects are small, only involving a few hectares, while others are far more ambitious, involving hundreds of hectares. Increasingly these projects are being coordinated at larger spatial scales in order to enhance biodiversity values at the landscape scale, especially for more mobile species such as birds. However, in almost all cases, some degree of predator management is also required either to ensure the success of plantings and regeneration, or to enhance habitats for indigenous fauna. The pervasive impact of predators on the New Zealand biota poses a number of important challenges for ecological restoration: Restoration goals need to be realistic and achievable. As elsewhere in the world, it is unrealistic to aim for restoration of a pre-human or even pre-European condition in most areas. Restoration goals that aim to sustain those things that are uniquely New Zealand within a context that recognises the realities of New Zealand today are likely to be more appropriate for most sites. Even with intensive predator control it is likely that we will increasingly be dealing with novel ecosystems resulting from restorative efforts. Restoration management needs to clearly identify all species that limit restoration success. Simply removing one predator such as stoats without addressing other species such as rats may well result in undesired outcomes for restoration. Furthermore, predator management needs to take into account the complex interactions that occur among different threats to biodiversity. Restoration management also needs to focus on the full range of ecosystems in New Zealand. There is much about New Zealand’s biodiversity that we do not know, and it is a certainty that many species are disappearing before they are even described. While much restoration work in New Zealand focuses on either highly-impacted lowland ecosystems or on the habitats of threatened vertebrate fauna (mainly birds), there are many other ecosystems that also require restorative management (e.g. hard beech forests and alpine grasslands). Finally, conservation planners need to ensure that the considerable resources involved in undertaking predator control are used to obtain the most sustainable biodiversity outcome. There are now and probably always will be insufficient resources available to target all predators everywhere in New Zealand, especially considering the substantial ongoing control costs. The sad reality of ecological restoration in New Zealand is that any let-up in predator control will most likely result in the loss of much, if not all, the gains of previous year’s hard work. While there is often talk about new research yielding ‘silver bullets’ that will solve the predator problem, experience suggests that this is unlikely to occur in the short to medium-term, and even if developed, is unlikely to deal with all invasive species, both plants and animals. One of the biggest challenges for New Zealand conservation is therefore deciding how best to allocate limited resources (both public and private) to ensure the most sustainable biodiversity outcome. It may well be that new approaches, for example, involving the private sector, will become increasingly important in New Zealand conservation, whereas a critical review needs to be undertaken of current approaches to invasive species management (e.g. the value of fenced versus un-fenced mainland island projects). The importance of targeted and sustainable resource allocation is particularly acute given ongoing declines of many elements of New Zealand’s indigenous biodiversity under current conservation management (Anon 2007). Notwithstanding the many problems that are faced in successfully implementing ecological restoration in New Zealand, there have been many success stories and there is no reason why there should not be many more in the future. Projects such as Tiritiri Matangi Island, Maungatautari Ecological Island, Rotoiti Nature Recovery Project and Hinewai Reserve, to name but a few, have been tremendous successes both ecologically and in terms of the involvement of and accessibility to the general public. The key for the future is for the many different groups involved in ecological restoration, government and non-government, business and non-business, to work together to ensure that the resources that are available are used in the most efficient manner possible so that New Zealand’s unique biodiversity is sustained.

Adapting ecosystem restoration for sustainable development in a changing world

Sandfish generations: Loss of genetic diversity due to hatchery practices in the sea cucumber Holothuria (Metriatyla) scabra

Effective population size reflects the history of population growth, contraction, and structuring. When the effect of structuring is negligible, the inferred trajectory of the effective population size can be informative about the key events in the history of a population. We used the IBDNe and DoRIS approaches, which exploit the data on IBD sharing between genomes, to reconstruct the recent effective population size in two population datasets of Russians from Eastern European plain: (1) ethnic Russians sampled from the westernmost part of Russia; (2) ethnic Russians, Bashkirs, and Tatars sampled from the Volga-Ural region. In this way, we examined changes in effective population size among ethnic Russians that reside in their historical area at the West of the plain, and that expanded eastward to come into contact with the indigenous peoples at the East of the plain. We compared the inferred demographic trajectories of each ethnic group to written historical data related to demographic events such as migration, war, colonization, famine, establishment, and collapse of empires. According to IBDNe estimations, 200 generations (~6000 years) ago, the effective size of the ancestral populations of Russians, Bashkirs, and Tatars hovered around 3,000, 30,000, and 8,000 respectively. Then, the ethnic Russians exponentially grew with increasing rates for the last 115 generations and become the largest ethnic group of the plain. Russians do not show any drop in effective population size after the key historical conflicts, including the Mongol invasion. The only exception is a moderate drop in the 17th century, which is well known in Russian history as The Smuta. Our analyses suggest a more eventful recent population history for the two small ethnic groups that came into contact with ethnic Russians in the Volga-Ural region. We found that the effective population size of Bashkirs and Tatars started to decrease during the time of the Mongol invasion. Interestingly, there is an even stronger drop in the effective population size that coincides with the expansion of Russians to the East. Thus, 15–20 generations ago, i.e. in the 16–18th centuries in the trajectories of Bashkirs and Tatars, we observe the bottlenecks of four and twenty thousand, respectively. Our results on the recent effective population size correlate with the key events in the history of populations of the Eastern European plain and have importance for designing biomedical studies in the region.

The influence of genetic drift on the formation and stability of polymorphisms arising from negative frequency-dependent selection

This study compares estimates of the census size of the spawning population with genetic estimates of effective current and long-term population size for an abundant and commercially important marine invertebrate, the brown tiger prawn (Penaeus esculentus). Our aim was to focus on the relationship between genetic effective and census size that may provide a source of information for viability analyses of naturally occurring populations. Samples were taken in 2001, 2002 and 2003 from a population on the east coast of Australia and temporal allelic variation was measured at eight polymorphic microsatellite loci. Moments-based and maximum-likelihood estimates of current genetic effective population size ranged from 797 to 1304. The mean long-term genetic effective population size was 9968. Although small for a large population, the effective population size estimates were above the threshold where genetic diversity is lost at neutral alleles through drift or inbreeding. Simulation studies correctly predicted that under these experimental conditions the genetic estimates would have non-infinite upper confidence limits and revealed they might be overestimates of the true size. We also show that estimates of mortality and variance in family size may be derived from data on average fecundity, current genetic effective and census spawning population size, assuming effective population size is equivalent to the number of breeders. This work confirms that it is feasible to obtain accurate estimates of current genetic effective population size for abundant Type III species using existing genetic marker technology.

Inconsistencies between equations for the effective population size of populations with separate sexes obtained by two different approaches are explained. One approach, which is the most common in the literature, is based on the assumption that the sex of the progeny cannot be identified. The second approach incorporates identification of the sexes of both parents and offspring. The approaches lead to identical expressions for effective size under some situations, such as Poisson distributions of offspring numbers. In general, however, the first approach gives incorrect answers, which become particularly severe for sex-linked genes, because then only numbers of daughters of males are relevant. Predictions of the effective size for sex-linked genes are illustrated for different systems of mating.

This study was accomplished on a more comprehensive basis to evaluate previous questions that were raised from a preliminary article about the genetic structure of Cryptocarya moschata populations. Thus, through the analysis of 40 polymorphic allozyme loci, allele frequencies were estimated from 335 individuals of 11 natural populations of C. moschata from six hydrographic basins of São Paulo state and Serra da Estrela, Rio de Janeiro, Brazil. Estimates of Wright's F statistics were done through the analysis of variance, presenting average values of <img border=0 width=32 height=32 id="_x0000_i1026" src="../../../../../../img/revistas/bn/v4n1/img/a04car(f).jpg" align=absmiddle > or = 0.352, <img border=0 width=32 height=32 id="_x0000_i1027" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle > or = 0.285 and <img border=0 width=32 height=32 id="_x0000_i1028" src="../../../../../../img/revistas/bn/v4n1/img/a04car(f2).jpg" align=absmiddle > or = 0.097. These results indicated that individuals within populations must be panmitic, and that the diversity among populations is fairly high, being superior to what would be expected for groups of plants having a full-sib family structure. From estimates of <img border=0 width=32 height=32 id="_x0000_i1029" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle>obtained for populations taken two at a time, the model of isolation by distance was tested; data did not fit the model, showing that <img border=0 width=32 height=32 id="_x0000_i1030" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle>did not increase by the respective increasing of the geographic distance. The estimated gene flow of 0.55 migrants per generation corroborated the pronounced populational differentiation, indicating that drift effects should be more important than the selection ones. The effective population sizes found from the sampled populations showed that there was an adequate genetic representativeness of the samples for those with relatively low values of <img border=0 width=32 height=32 id="_x0000_i1031" src="../../../../../../img/revistas/bn/v4n1/img/a04car(f2).jpg" align=absmiddle>. Though, under a metapopulation context, the effective population size was 17.07 individuals, indicating that sampling performed for the species corresponded to 88.44% of the maximum effective size obtained from 11 populations with a <img border=0 width=32 height=32 id="_x0000_i1032" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle>of 0.285, equivalent to only 5.09% individuals for the total sampled. Management and conservation strategies aimed at preserving high intrapopulation genetic variation in C. moschata would imply in the maintenance of populations with great number of individuals. Moreover, for the preservation of the species as a whole, the maintenance of many such populations would be mandatorily recommended, which denotes that the conservation of large areas of Atlantic rain forest should be necessary to hold its evolutionary dynamics.

Genomic selection has been applied in dairy cattle breeding over the last decade. Using genomic information may speed up genetic gain as breeding values can be predicted reasonably accurately directly after birth. However, genetic diversity may decrease if the inbreeding rate per generation increases and the effective population size decreases. Despite many positive qualities of the Finnish Ayrshire, for example, high average protein yield and fertility, over time the breed has lost its place as the most common dairy breed in Finland. Thus, maintaining the genetic variability of the breed is becoming more important. The aim of our research was to estimate the impact of genomic selection on inbreeding rate and effective population size using both pedigree and genomic data. The genomic data included 46,914 imputed single nucleotide polymorphism (SNP) variants from 75,038 individuals, and the pedigree data included 2,770,025 individuals. All animals in the data were born between 2000 and 2020. Genomic inbreeding coefficients were estimated as the proportion of SNPs in runs of homozygosity (ROH) out of the total number of SNPs. The inbreeding rate was estimated by regressing the mean genomic inbreeding coefficients on birth years. Effective population size was then estimated based on the inbreeding rate. Additionally, effective population size was estimated from the mean increase in individual inbreeding using pedigree data. Introduction of genomic selection was assumed to have taken place gradually; years 2012-2014 were treated as a transition period from the traditional phenotype-based breeding value estimation to genomic-based estimation. The median length of the identified homozygous segments was 5.5Mbp, and a slight increase in the proportion of segments over 10Mbp was observed after 2010. The inbreeding rate decreased from 2000 to 2011 and subsequently increased slightly. The pedigree- and genomic-based estimates of inbreeding rate were similar to each other. The estimates of effective population size based on the regression method were very sensitive to the number of years considered; thus, the estimates were not very reliable. The effective population size estimated from the mean increase in individual inbreeding reached its highest value of 160 in 2011 and decreased to 150 after that. In addition, the generation interval in the sire path has decreased from 5.5 years to 3.5 years after genomic selection was implemented. Based on our results, after the implementation of genomic selection, the proportion of long ROH stretches has increased, the generation interval in the sire path has decreased, the inbreeding rate has increased and the effective population size has decreased. However, the effective population size is still at a good level, allowing for an efficient selection scheme in the Finnish Ayrshire breed.